Maternal Transmission Ratio Distortion in Two Iberian Pig Varieties
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals, Data, and Ethics Statements
2.2. Transmission Ratio Distortion Analysis
2.3. Analysis of Gene Enrichment
2.4. Data Availability
3. Results and Discussion
3.1. Estimates of Maternal Transmission Ratio Distortion Loci
3.2. Possible Biological Implications of Transmission Ratio Distortion Loci
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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ID Marker | Chr | Pos (Mb) | TRD_E | q-val_E | CallR_E | TRD_R | q-val_R | CallR_R | Gene with TRD Locus |
---|---|---|---|---|---|---|---|---|---|
rs339672482 | 2 | 12.698 | −0.495 | 8.5 × 10−36 | 100.0 | −0.495 | 1.8 × 10−33 | 100.0 | ENSSSCG00000031496 |
rs343381067 | 2 | 14.467 | −0.495 | 5.3 × 10−34 | 98.9 | −0.409 | 1.4 × 10−15 | 99.4 | ENSSSCG00000031436 |
rs335768329 | 4 | 83.114 | −0.378 | 1.3 × 10−12 | 96.6 | −0.495 | 8.8 × 10−28 | 94.5 | ADCY10 |
rs81476539 | 6 | 72.737 | −0.402 | 1.3 × 10−16 | 100.0 | −0.322 | 4.1 × 10−08 | 100.0 | |
rs324128272 | 9 | 2.722 | −0.473 | 4.8 × 10−24 | 99.4 | −0.447 | 5.5 × 10−23 | 99.4 | |
rs346413844 | 9 | 11.795 | −0.367 | 1.8 × 10−10 | 93.7 | −0.346 | 5.2 × 10−11 | 97.8 | |
rs319847656 | 9 | 23.041 | −0.453 | 4.3 × 10−21 | 99.4 | −0.495 | 1.8 × 10−33 | 100.0 | ENSSSCG00000049020 |
rs344225789 | 18 | 49.209 | −0.439 | 5.5 × 10−20 | 99.4 | −0.252 | 0.0131 | 99.4 | |
rs331690240 | 20 | 14.2345 | −0.278 | 1.4 × 10−05 | 100.0 | −0.26 | 1.2 × 10−04 | 99.4 | ENSSSCG00000050465 |
rs343278080 | 20 | 26.079 | −0.265 | 0.0231 | 100.0 | −0.485 | 1.8 × 10−29 | 100.0 |
ID Marker | Chromosome | Position (b) | Gene with TRDL | Iberian Variety | Marker Call Rate |
---|---|---|---|---|---|
rs337916686 | 1 | 162,977,295 | ATP8B1 | Entrepelado | 100.0 |
rs80864027 | 1 | 163,382,446 | IGDCC4 | Entrepelado | 100.0 |
rs81305791 | 1 | 271,207,043 | NUP214 | Entrepelado | 100.0 |
rs339672482 | 2 | 12,697,523 | ENSSSCG00000031496 | Entrepelado | 100.0 |
rs343381067 | 2 | 14,467,327 | ENSSSCG00000031436 | Entrepelado | 98.9 |
rs81221692 | 3 | 102,885,453 | PRKD3 | Entrepelado | 100.0 |
rs335768329 | 4 | 83,113,768 | ADCY10 | Entrepelado | 96.6 |
rs81385903 | 5 | 83,334,157 | ANO4 | Entrepelado | 100.0 |
rs55618893 | 5 | 91,751,676 | LUM | Entrepelado | 100.0 |
rs320534160 | 7 | 1,148,169 | GMDS | Entrepelado | 100.0 |
rs80939667 | 7 | 7,368,476 | GCNT2 | Entrepelado | 100.0 |
rs338044350 | 7 | 7,378,724 | GCNT2 | Entrepelado | 100.0 |
rs327255612 | 8 | 4,896,260 | EVC2 | Entrepelado | 100.0 |
rs81420408 | 9 | 2,210,850 | SYT9 | Entrepelado | 100.0 |
rs319847656 | 9 | 23,040,656 | ENSSSCG00000049020 | Entrepelado | 99.4 |
rs81262274 | 9 | 135,247,805 | ENSSSCG00000031141 | Entrepelado | 100.0 |
rs335996850 | 10 | 24,233,693 | RNPEP | Entrepelado | 100.0 |
rs320095885 | 14 | 42,820,750 | SGSM1 | Entrepelado | 100.0 |
rs80994847 | 14 | 43,934,858 | SEZ6L | Entrepelado | 100.0 |
rs334182161 | 18 | 3,613,926 | DPP6 | Entrepelado | 100.0 |
rs327443567 | 18 | 17,971,591 | ENSSSCG00000051610 | Entrepelado | 100.0 |
rs326744865 | 18 | 18,486,229 | CPA1 | Entrepelado | 100.0 |
rs331690240 | 20 | 14,234,646 | ENSSSCG00000050465 | Entrepelado | 100.0 |
rs320767193 | 20 | 120,168,429 | ENSSSCG00000042120 | Entrepelado | 100.0 |
rs80947114 | 1 | 252,918,477 | SUSD1 | Retinto | 100.0 |
rs333078973 | 1 | 268,840,777 | CERCAM | Retinto | 100.0 |
rs339672482 | 2 | 12,697,523 | ENSSSCG00000031496 | Retinto | 100.0 |
rs343381067 | 2 | 14,467,327 | ENSSSCG00000031436 | Retinto | 99.4 |
rs323787335 | 4 | 7,369,788 | ZFAT | Retinto | 100.0 |
rs335768329 | 4 | 83,113,768 | ADCY10 | Retinto | 94.5 |
rs81414835 | 9 | 9,862,005 | MAP6 | Retinto | 99.4 |
rs81414870 | 9 | 9,898,353 | MAP6 | Retinto | 99.4 |
rs342178816 | 9 | 11,759,440 | ENSSSCG00000014877 | Retinto | 100.0 |
rs319847656 | 9 | 23,040,656 | ENSSSCG00000049020 | Retinto | 100.0 |
rs81280147 | 9 | 99,713,062 | CD36 | Retinto | 100.0 |
rs331690240 | 20 | 14,234,646 | ENSSSCG00000050465 | Retinto | 99.4 |
GO ID | Term | Genes Found | Fold Enrichment | p-Value Corrected |
---|---|---|---|---|
GO:0030307 | Cell growth | 1 | 56.78 | 0.0217 |
GO:0097061 | Dendrite | 1 | 56.78 | 0.0217 |
GO:0043542 | Endothelial cell migration | 1 | 45.42 | 0.026 |
GO:0048332 | Mesoderm morphogenesis | 1 | 22.71 | 0.0472 |
GO:0045216 | Cell-cell junction | 2 | 18.17 | 0.00622 |
GO:0050770 | Axonogenesis | 2 | 10.32 | 0.0174 |
GO:0010975 | Neuron development | 2 | 6.88 | 0.0359 |
GO:0000904 | Cell morphogenesis | 4 | 5.05 | 0.00881 |
GO:0000902 | Cell morphogenesis | 5 | 4.38 | 0.00617 |
GO:0009653 | Morphogenesis | 6 | 2.98 | 0.0163 |
GO ID | Term | Entrepelado Variety | Retinto Variety | ||||
---|---|---|---|---|---|---|---|
Genes Found | Fold Enrichment | p-Value Corrected | Genes Found | Fold Enrichment | p-Value Corrected | ||
GO:0060048 | Cardiac muscle | 3 | 8.91 | 0.00649 | |||
GO:0048813 | Dendrite | 2 | 8.41 | 0.0294 | |||
GO:0002088 | Eye | 3 | 7.57 | 0.00966 | |||
GO:0050953 | Light stimulus | 3 | 7.57 | 0.00966 | |||
GO:0034968 | Histone-lysine methylation | 3 | 7.21 | 0.0109 | |||
GO:0050803 | Synapse structure | 3 | 6.88 | 0.0122 | 2 | 9.47 | 0.0216 |
GO:0045216 | Cell-cell junction | 3 | 6.06 | 0.0166 | 2 | 8.33 | 0.027 |
GO:0017156 | Calcium | 3 | 5.41 | 0.0219 | |||
GO:0051592 | Calcium | 3 | 4.73 | 0.0301 | |||
GO:0050770 | Axonogenesis | 4 | 4.59 | 0.014 | 3 | 7.1 | 0.0101 |
GO:0015850 | Compound transport | 4 | 4.49 | 0.015 | |||
GO:0055002 | Striated muscle | 3 | 4.45 | 0.0348 | |||
GO:0010975 | Neuron development | 5 | 3.82 | 0.0123 | 3 | 4.74 | 0.0281 |
GO:0099504 | Synapse structure | 4 | 3.11 | 0.0453 | |||
GO:0000904 | Cell morphogenesis | 8 | 2.24 | 0.031 | 5 | 2.89 | 0.0322 |
GO:0009653 | Morphogenesis | 19 | 2.1 | 0.00348 | 7 | 1.6 | 0.218 |
GO:0000902 | Cell morphogenesis | 10 | 1.95 | 0.0432 | 6 | 2.41 | 0.0416 |
GO:0030307 | Cell growth | 1 | 26.05 | 0.0466 | |||
GO:0097061 | Dendrite | 1 | 26.05 | 0.0466 | |||
GO:0009247 | Lipid biosynthesis | 4 | 13.02 | 0.000369 | |||
GO:0044255 | Lipid metabolism | 9 | 3.14 | 0.00285 | |||
GO:0007606 | Chemical stimulus | 8 | 3.35 | 0.0033 | |||
GO:0046467 | Lipid biosynthesis | 4 | 6.72 | 0.00361 | |||
GO:0030148 | Lipid biosynthesis | 3 | 8.93 | 0.0056 | |||
GO:0007186 | Receptor | 16 | 1.94 | 0.0117 | |||
GO:0031623 | Receptor | 2 | 10.42 | 0.0183 | |||
GO:0007584 | Response to nutrient | 1 | 26.05 | 0.0466 | |||
GO:0015909 | Lipid transport | 1 | 26.05 | 0.0466 |
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Vázquez-Gómez, M.; Hijas-Villalba, M.M.d.; Varona, L.; Ibañez-Escriche, N.; Rosas, J.P.; Negro, S.; Noguera, J.L.; Casellas, J. Maternal Transmission Ratio Distortion in Two Iberian Pig Varieties. Genes 2020, 11, 1050. https://doi.org/10.3390/genes11091050
Vázquez-Gómez M, Hijas-Villalba MMd, Varona L, Ibañez-Escriche N, Rosas JP, Negro S, Noguera JL, Casellas J. Maternal Transmission Ratio Distortion in Two Iberian Pig Varieties. Genes. 2020; 11(9):1050. https://doi.org/10.3390/genes11091050
Chicago/Turabian StyleVázquez-Gómez, Marta, Melani Martín de Hijas-Villalba, Luis Varona, Noelia Ibañez-Escriche, Juan Pablo Rosas, Sara Negro, José Luis Noguera, and Joaquim Casellas. 2020. "Maternal Transmission Ratio Distortion in Two Iberian Pig Varieties" Genes 11, no. 9: 1050. https://doi.org/10.3390/genes11091050